def run_0(symbol = "C 2"):
space_group_info = sgtbx.space_group_info(symbol = symbol)
xrs = random_structure.xray_structure(
space_group_info = space_group_info,
elements = ["N"]*50,
volume_per_atom = 100.0,
random_u_iso = True)
#
b_cart = adptbx.random_traceless_symmetry_constrained_b_cart(
crystal_symmetry=xrs.crystal_symmetry())
u_star = adptbx.u_cart_as_u_star(xrs.unit_cell(), adptbx.b_as_u(b_cart))
#
F = xrs.structure_factors(d_min = 1.5).f_calc()
k_anisotropic = mmtbx.f_model.ext.k_anisotropic(F.indices(), u_star)
#
bin_selections = []
F.setup_binner(reflections_per_bin=50)
for i_bin in F.binner().range_used():
sel = F.binner().selection(i_bin)
bin_selections.append(sel)
#
d_spacings = F.d_spacings().data()
ss = 1./flex.pow2(d_spacings) / 4.
k_mask_tmp = mmtbx.f_model.ext.k_mask(ss, 0.35, 80.)
k_mask = flex.double(F.data().size(), 0)
k_isotropic = flex.double(F.data().size(), 0)
for s in bin_selections:
d = d_spacings.select(s)
k_mask.set_selected(s, flex.mean(k_mask_tmp.select(s)))
k_isotropic.set_selected(s, random.randint(1,10))
#
fmodel = mmtbx.f_model.manager(
xray_structure = xrs,
f_obs = abs(F),
k_isotropic = k_isotropic,
k_anisotropic = k_anisotropic,
k_mask = k_mask)
f_calc = fmodel.f_calc()
f_masks = fmodel.f_masks()
f_model = fmodel.f_model()
f_obs = abs(f_model)
r_free_flags = f_obs.generate_r_free_flags(use_lattice_symmetry=False)
#
assert approx_equal(bulk_solvent.r_factor(f_obs.data(), f_model.data()), 0)
aso = scaler.run(
f_obs = f_obs,
f_calc = f_calc,
f_mask = f_masks,
r_free_flags = r_free_flags,
bin_selections = bin_selections,
number_of_cycles = 500,
auto_convergence_tolerance = 1.e-9,
ss = ss,
try_poly = True,
try_expanal = True,
try_expmin = True,
verbose = False)
assert approx_equal(aso.r_final, 0.00037, 0.00001)
assert approx_equal(aso.r_low, 0.00002, 0.00001)
assert approx_equal(aso.r_high, 0.00006, 0.00001)
assert approx_equal(
bulk_solvent.r_factor(f_obs.data(), abs(aso.core.f_model).data(), 1),
bulk_solvent.r_factor(f_obs.data(), abs(aso.core.f_model).data()))
def run_0(symbol="C 2"):
space_group_info = sgtbx.space_group_info(symbol=symbol)
xrs = random_structure.xray_structure(space_group_info=space_group_info,
elements=["N"] * 50,
volume_per_atom=100.0,
random_u_iso=True)
#
b_cart = adptbx.random_traceless_symmetry_constrained_b_cart(
crystal_symmetry=xrs.crystal_symmetry())
u_star = adptbx.u_cart_as_u_star(xrs.unit_cell(), adptbx.b_as_u(b_cart))
#
F = xrs.structure_factors(d_min=1.5).f_calc()
k_anisotropic = mmtbx.f_model.ext.k_anisotropic(F.indices(), u_star)
#
bin_selections = []
F.setup_binner(reflections_per_bin=50)
for i_bin in F.binner().range_used():
sel = F.binner().selection(i_bin)
bin_selections.append(sel)
#
d_spacings = F.d_spacings().data()
ss = 1. / flex.pow2(d_spacings) / 4.
k_mask_tmp = mmtbx.f_model.ext.k_mask(ss, 0.35, 80.)
k_mask = flex.double(F.data().size(), 0)
k_isotropic = flex.double(F.data().size(), 0)
for s in bin_selections:
d = d_spacings.select(s)
k_mask.set_selected(s, flex.mean(k_mask_tmp.select(s)))
k_isotropic.set_selected(s, random.randint(1, 10))
#
fmodel = mmtbx.f_model.manager(xray_structure=xrs,
f_obs=abs(F),
k_isotropic=k_isotropic,
k_anisotropic=k_anisotropic,
k_mask=k_mask)
f_calc = fmodel.f_calc()
f_masks = fmodel.f_masks()
f_model = fmodel.f_model()
f_obs = abs(f_model)
r_free_flags = f_obs.generate_r_free_flags(use_lattice_symmetry=False)
#
assert approx_equal(bulk_solvent.r_factor(f_obs.data(), f_model.data()), 0)
aso = scaler.run(f_obs=f_obs,
f_calc=f_calc,
f_mask=f_masks,
r_free_flags=r_free_flags,
bin_selections=bin_selections,
number_of_cycles=500,
auto_convergence_tolerance=1.e-9,
ss=ss,
try_poly=True,
try_expanal=True,
try_expmin=True,
verbose=True)
print("r_f:", aso.r_final)
print("r_l:", aso.r_low)
print("r_h:", aso.r_high)
assert aso.r_final < 0.0009, [aso.r_final, 0.0009]
assert aso.r_low < 0.0017, [aso.r_low, 0.0017]
assert aso.r_high < 0.0006, [aso.r_high, 0.0006]
assert approx_equal(
bulk_solvent.r_factor(f_obs.data(),
abs(aso.core.f_model).data(), 1),
bulk_solvent.r_factor(f_obs.data(),
abs(aso.core.f_model).data()))